Browsing by Author "Underhill, Les"

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    A comparative study of stochastic models in biology
    (1997) Brandão, Anabela de Gusmão; Zucchini, Walter; Underhill, Les
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    A comparative study of stochastic models in biology
    (1997) Brandão, Anabela de Gusmão; Zucchini, Walter; Underhill, Les
    In many instances, problems that arise in biology do not fall under any category for which standard statistical techniques are available to be able to analyse them. Under these situations, specifics methods have to be developed to solve and answer questions put forward by biologists. In this thesis four different problems occurring in biology are investigated. A stochastic model is built in each case which describes the problem at hand. These models are not only effective as a description tool but also afford strategies consistent with conventional model selection processes to deal with the standard statistical hypothesis testing situations. The abstracts of the papers resulting from these problems are presented below.
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    The African penguin Spheniscus demersus : conservation and management issues
    (2011) Waller, Lauren; Underhill, Les
    The African penguin is a southern African endemic, with its breeding distribution within the Benguela Upwelling Ecosystem. The IUCN conservation status of this species was re-classified from ‘Vulnerable’ to ‘Endangered’ in 2010. This thesis investigated some aspects pertinent to the species’ conservation and management. Time series of population estimates of African penguins and fish biomass were available in South Africa since the late 1980s. This study analysed the fish biomass at a stratum scale, which is a finer scale to that of previous studies which looked at biomass estimates as a whole. The strata range in length from c. 155 km to c. 280 km in length. The number of African penguin breeders and adult moulters were found to be positively correlated with fish biomass estimates, although results of the spatial relationships were unexpected. The islands which displayed the strongest relationships were Dassen Island and Robben Island. These islands are only c. 50 km apart, and it is expected that they would experience similar oceanographic conditions. However, the colonies at these islands were found to respond differently to fish biomass estimates. While the number of Dassen Island birds were found to be positively correlated with biomass estimates within the strata in which the island is found, the number of Robben Island birds were correlated with biomass estimates of the stratum to the south and east of the island. Weaker relationships were found for the remaining colonies. This study suggested that the period of moult is of critical importance to the survival of the penguin, an aspect that needs to be incorporated into the Ecosystem Approach to Fisheries modelling.
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    Analysis of distribution maps from bird atlas data: dissimilarities between species, continuity within ranges and smoothing of distribution maps
    (1998) Erni, Birgit; Underhill, Les
    A dissimilarity coefficient for estimating the dissimilarity between two bird atlas distributions is developed. This coefficient is based on the Euclidean distance concept. The atlas distributions are compared over all quarter degree grid cells. Existing coefficients are not suitable for the comparison of distributions with different total areas and species with different mean reporting rates. In each grid cell the reliability of the reporting rates depends on the number of checklists collected for the grid cell. Weights are used to solve this problem. To solve the problem of different levels of abundance and conspicuousness of species, the reporting rates are sorted into percentiles, using five or 10 categories for the strictly positive reporting rates. Each grid cell is weighted by a function of the number of checklists collected for the grid cell. The coefficient is scaled by the maximum possible sum of the differences which would occur if there is no overlap between the two distributions, so that the dissimilarity coefficient lies between zero (a perfect match) and one (no overlap). A variety of these coefficients are investigated and compared. The continuity of observed reporting rates in a spatial cellular map is an indication of spatial autocorrelation present, especially between observations which are in close vicinity. We are particularly interested in measuring and comparing the continuity of the reporting rates in the bird distributions from The Atlas of Southern African Birds. The variogram, developed in geostatistics, estimates this spatial autocorrelation. The classical variogram estimator, however, is dependent on the scale of measurement and assumes that the data are intrinsically stationary. The bird atlas distribution maps contain trend and the variance of each observation (reporting rate) is a function of the number of checklists collected for the grid cell and the underlying probability of encountering the species in the grid cell. The approach of removing this binomial measurement error from the variogram developed by McNeill (1991) is investigated but not found satisfactory. A weighted variogram, where each squared difference is weighted by a function of the smaller number of checklists, is developed. To make the variogram values comparable between species a function of the mean reporting rates is used to scale the variogram. We were particularly interested in the first variogram value of each species distribution, 2y(1). The bird distribution maps in The Atlas of Southern African Birds show the raw observed reporting rates. Each of these reporting rates is a random variable dependent on sampling error due to binomial variation based on the number of checklists collected for the grid cell and on the underlying probability of encountering the species. The distribution maps show this measurement error. It is believed that a smoothed version of the bird distribution maps will to some extent improve the statement these observed distributions are aiming to make. Single-step regression methods are investigated for a fast approach to this problem. These cause problems because of frequent 'zero' observed reporting rates and because they smooth the maps too heavily. Generalized Linear Models are investigated and this iterative procedure is applied to model the reporting rates with a binomial distribution on square blocks of nine grid cells where a value for the central cell is 'predicted' in each regression. This approach is especially suited to accommodate the binomial distribution characteristics and is found to smooth the bird atlas distributions well. Because only a local window is taken for each regression, the spatial autocorrelation is adequately included in the spatial explanatory variables.
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    Application of ANOVA for the analysis of temporal and spatial differences in the length of pelagic goby preyed on by Cape fur seals in the coasts of Namibia
    (2005) Anday, Tekie T; Underhill, Les; Kirkman, Silvia
    The Analysis of variance is a robust technique whereby the total variation present in a set of data is partitioned into two or more components (Wayne, 1999). In this thesis, ANOVA was used to uncover the differences in goby length preyed on by three different colonies of fur seals at the Namibian coast. Moreover, ANOVA was used to investigate temporal differences in lengths of goby preyed on by fur seals in each location of the seal colonies. Results of the analysis are shown in the Analysis and results section, and the findings are discussed in the discussion section. But before these two sections, there are three sections of the thesis. The first section is the general introduction that explains about the general situation and the targets of this thesis. The second section gives a general background on the ANOVA technique. The third section explains the nature of the data and gives background information on gobies.
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    Assessing the conservation value of wetlands and waterbirds with a focus on the winter rainfall region of South Africa
    (2012) Harebottle, Douglas Michael; Underhill, Les
    This thesis deals with the development and application of a new tool to assess the conservation significance of wetland avifauna. Termed the Waterbird Conservation Value (WCV) score, this method sums the proportion of each species' count relative to the global 1% threshold level for each species; the value obtained measures the overall conservation importance of the wetland to waterbirds.
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    The biology and conservation of the Damara Tern in Namibia
    (2011) Braby, Justine; Underhill, Les; Simmons, Robert E; Roux, Jean-Paul
    The globally Near-threatened Damara Tern Sterna balaenarum is little known and faces several conservation issues. The aim of this study was to provide a description of the ecology and numbers of the species and discuss conservation management plans that will effectively ensure its survival.
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    Breeding production of Cape gannets Morus capensis at Malgas Island, 2002-03
    (2006) Staverees, Linda; Underhill, Les; Crawford, RJM
    Includes bibliographical references.
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    The Cape fur seal : monitoring and management in the Benguela Current ecosystem
    (2010) Kirkman, Stephen Patrick; Underhill, Les
    At the root of this thesis was the Benguela Current Large Marine Ecosystem (BCLME) Programme’s project "Top Predators as Biological Indicators of Ecosystem Change in the BCLME" (LMR/EAF/03/02). The objectives of this project were to assess the utility of top predators as biological indicators of ecosystem change in the Benguela Current Ecosystem, and implement an appropriate, integrated, system-wide monitoring programme based on top predators, to support ecosystem-based management in the Benguela Current Ecosystem.
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    Citizen Science - building an early warning system for biodiversity
    (2012) Underhill, Les
    Lecture series coordinated by Professor Les Underhill, Director, Animal Demography Unit, Department of Zoology, UCT. This lecture series studies a number of animal demography initiatives underway in South Africa, and highlights the ways in which members of the public can get involved in scientific and conservation efforts by volunteering their time. This lecture series will be of interest to aspiring citizen scientists, zoologists and others working in the field of biodiversity.
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    Cold winters vs long journeys : adaptations of primary moult and body mass to migration and wintering in the Grey Plover Pluvialis Squatarola
    (2002) Serra, Lorenzo; Underhill, Les
    The Grey Plover Pluvialis squatarola is a circumpolar breeding wader with a cosmopolitan winter distribution. Primary moult generally starts only when potential wintering sites are reached. Across the Palearctic-African region Grey Plovers experience an enormous variety of ecological and climatic conditions, which determine the development of different moult patterns, according to local conditions and timing of migration.
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    The diet of the Cape fur seal Arctocephalus pusillus pusillus in Namibia : variability and fishery interactions
    (2005) Mecenero, Silvia; Underhill, Les; Roux, Jean-Paul; Crawford, RJM; Bester, MN
    Includes bibliographical references.
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    The effects of environment and niche on the distributions of dwarf chameleons, present and future
    (2007) Houniet, Darren; Underhill, Les; Thuiller, Wilfried; Tolley, Krystal A; Midgley, Guy
    The niche and niche breadth of Dwarf Chameleons, Bradypodion, was assessed in terms of broad scale climatic factors. A niche-based modelling method was then used to construct present and future habitat suitability maps for 2050 and 2080, for species in the genus. Additionally, the relationship between environment and morphology was analysed for a representative Bradypodion species, the Cape Dwarf Chameleon, B. pumilum. The niche and niche breadth of species and phylogenetic clades were analysed and described via an ordination technique, the outlying mean index (OMI) analysis. Maxent (v2.3), a presence only niche modelling method, proved very useful in the construction of present and future habitat suitability maps for species within the genus. For analysis of the correspondence between environment and morphology for B. pumilum, regression trees were employed. Rainfall seasonality and maximum annual temperatures were shown to strongly effect the current distributions of the genus Bradypodion at both the species and clade level. Additionally, as closely related species inhabited similar environmental niches, the genus was shown to display a degree of niche conservatism. All species and clades were shown to respond to climate change scenarios for 2050 and 2080, but responses were individualistic. However, most demonstrated range contractions under predicted climate scenarios. Additionally, a strong correlation (p < 0.05) was found between the morphology of B. pumilum and its environment. Environmental factors explained over 40% of the variation in snout-vent length and tail length, and over 20% of the variation in head width and head height, thus supporting the hypothesis of a correspondence between vegetation and morphology in Bradypodion. These results have provided an understanding of the relationship between Bradypodion and their environments that could provide valuable information regarding their ecology. Additionally, the habitat suitability maps for 2050 and 2080 could prove useful in the construction of any future conservation plans for these species. Furthermore, the results support the hypothesis of a correspondence between environmental factors and morphological traits within the genus Bradypodion.
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    The effects of oiling and rehabilitation on the breeding productivity and annual moult and breeding cycles of African penguins
    (2007) Wolfaardt, Anton Carl; Underhill, Les
    Includes bibliographical references.
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    The effects of prey availability on the endangered bank cormorant Phalacroxorax neglectus
    (2014) Botha, Philna; Underhill, Les; Ryan, Peter G; Sherley, Richard; Cook, Timothée
    The bank cormorant Phalacrocorax neglectus is a seabird endemic to the south-western coast of southern Africa and the Benguela Upwelling System and has suffered a decline of more than 50% over three generations. Main threats include displacement by Cape fur seals Arctocephalus pusillus, direct human disturbance, pollution, climate change and food shortage. This thesis focuses on the bank cormorant’s response to food shortage, both directly and indirectly. Four colonies (Jutten Island, Dassen Island, Robben Island and Stony Point) were studied in terms of responses on population level in relation to the spatial distribution of prey surrounding the various colonies, foraging behaviour and breeding success. First, I tested the response of the bank cormorant ’ s population dynamics in relation to the availability of West Coast rock lobster Jasus lalandii in different spatial scales around three colonies (Jutten Island, Dassen Island and Stony Point) over a subset of years. I found that birds at Dassen Island showed the strongest response to the availability of rock lobster. Birds also showed strongest response to the availability of rock lobster in an accumulative distance around colonies, and their largest response was to rock lobster within 30 km distance from the colony. Various aspects including the life - history traits and moulting stages of this particular rock lobster species may be the reason to this response. Second, I present foraging effort data of bank cormorants in localities known to be situated in areas with different prey availability. I found that at Jutten Island, situated in an area where West Coast rock lobster have dramatically decreased, bank cormorants spent significantly longer time at sea than at Robben Island and Stony Point, which were situated in areas where rock lobster were known to be abundant at the time of the study. Third, I tested the effect of food availability on the breeding success of bank cormorants at Jutten Island, Robben Island and Stony Point. There was no significant relationship between food availability and the survival probability of the birds. The number of chicks fledged per successful nest, however was significantly related to the availability of rock lobster during the relevant breeding season, as well as during the relevant month of hatching.
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    The effects of white shark presence on the behaviour of Cape fur seals at Geyser Rock, Gansbaai, South Africa
    (2013) Wcisel, Michelle; O'Riain, Justin; De Vos, Alta; Underhill, Les
    Predators and the risk associated with their presence may affect group composition, group size, movement patterns, and habitat use of prey species. The removal of predators, or their reintroduction following long periods of absence, equally can have profound impacts on their prey, triggering ecological cascades and ultimately shaping the biota of entire landscapes. While such processes are well documented in terrestrial ecosystems, similar results are absent in the marine realm, largely due to logistical difficulty. One exception to this is the study of white shark and seal interactions at coastal island rookeries, where white shark presence is seasonal, and seals exhibit marked behavioural differences between seasons. What is lacking from these studies, however, is how subsurface habitat around the islands, specifically refugia, may influence the behaviour of seals and their interactions with white sharks. I address this challenge by comparing both seal movement patterns and shark-seal interactions at Geyser Rock, Gansbaai with the established seal and shark patterns at Seal Island, False Bay. White sharks aggregate at both islands during the austral winter and seals encounter these aggregations when commuting to and from their respective rookeries to offshore foraging areas. The seascape around Geyser Rock is comparably more featured, including kelp beds and extensive shallow (5-10m depth) reef systems, whereas Seal Island is largely featureless, with neither extensive kelp nor reefs. At Geyser Rock, predations by white sharks were rarely observed (0.1 predations/hour) compared to Seal Island (1.24 predations/hour) and lacked the focused spatiotemporal peak at sunrise to the south of the island. Seals at Geyser Rock did not show a relationship between group formation and season, which was clearly demonstrated at Seal Island. This suggests that seals at Geyser Rock may be less reliant on group formation (safety in numbers) and selfish herd tactics within such groups to reduce predation risk. Rather, seals at Geyser Rock avoided deep open water patches during winter and shifted their movement patterns to and from the island to sectors with greater subsurface habitat heterogeneity. While I was limited in quantifying spatiotemporal patterns of predation risk around Geyser Rock (predation events were rare and widely dispersed), these results strongly suggest that seals actively avoid deep open water and show a preference for high structural complexity sectors during the risky winter months when shark presence is highest. This finding represents a habitat-escape tactic unidentified in previously studied white shark/pinniped systems. Together these results provide empirical support for both the risk-allocation hypothesis and refugia hypotheses within marine predator-prey systems.
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    The endangered bank cormorant Phalacrocorax neglectus: the heat is on : understanding the effect of climate change and associated environmental variable changes on the breeding biology and population dynamics of the bank cormorant in the W. C., S. A
    (2014) Meyer,Corlia; Underhill, Les; Ryan, Peter G; Sherley, Richard; Cook, T
    The bank cormorant Phalacrocorax neglectus was listed as ‘Endangered’ in 2004, following a decrease of more than 60% in the total population from 1975-2011. It ranges from central Namibia to the Western Cape, South Africa, with most of the population occurring on offshore islands in Namibia. The main reason for this study was to determine if climate change could be identified as a factor which has influenced the decreasing numbers of bank cormorants. This involved research on the heat stress behaviour, breeding success and population trends of the bank cormorant in the Western Cape, South Africa. High environmental temperatures resulting in heat stress and storms with associated extreme environmental variables was predicted to cause breeding failures, decreasing breeding success. As a result, climate change can also affect long-term trends in the adult population of the bank cormorant, and this was examined using the population data of nine bank cormorant colonies in the Western Cape, South Africa. A link existed between ambient and operative temperature, and the latter was used for statistical analysis. Mean operative temperatures of over 30°C were experienced. Temperatures were highest at the bank cormorant colony at Robben Island when three colonies were compared (Robben Island, Jutten Island and Stony Point). Increased environmental temperatures resulted in the average bank cormorant increasing its time spent employing thermoregulatory behaviour. Bank cormorants were shown to start gular fluttering at 21°C on average and spend all their time gular fluttering when they experienced an operative temperature of 34.2°C or higher. The birds also started employing this thermoregulatory behaviour at a lower temperature when on eggs or small chicks. During the study period, the breeding success of the bank cormorant was not impacted by high temperatures at the three bank cormorant colonies studied. Wave and wind action, associated with storms, resulted in a lowered reproductive output during the breeding seasons of 2012 and 2013. Both incubation success and chick rearing success did not differ significantly between 2012 and 2013 for the three bank cormorant colonies at Robben Island, Jutten Island and Stony Point. The study of long-term trends in colony sizes of nine bank cormorant colonies in the Western Cape, South Africa revealed a decrease in the bank cormorants breeding population. The decrease could not be directly associated with climate change in the region. An increase in the mean maximum temperatures and a decrease in the annual rainfall did not affect the bank cormorant numbers, but rather the fecundity. This resulted in a lagged effect of climate change on the bank cormorant population. Climate change and extreme weather events can cause massive breeding failures.
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    Energy budget and foraging behaviour of the Cape gannet Morus capensis during the breeding season
    (2010) Navarro-Canas, Rene Alfredo; Underhill, Les
    This thesis deals with the energy expenditure of free-ranging Cape gannets Morus capensis breeding at Malgas Island, South Africa. I sought to determine the energy budget of family units and to extrapolate this to the whole population. Energy expenditure was measured using the doubly labelled water technique on adults and chicks. CO2 production was determined from ratios of isotope turnover, and converted into energy expenditure using a factor suitable for a fish-eating seabird.
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    Evaluating a citizen science research programme : understanding the people who make it possible
    (2011) Wright, Dale; Underhill, Les
    Citizen science is increasingly recognised as a useful tool for conducting scientific research and public outreach, producing multiple positive benefits for biodiversity conservation and the volunteers involved in such research.